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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atagttctgtcatgtcattgagggctttctgttatctctgttcattcattatattgatttatggtcatgttgaaggtaagctcacttgctactaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAAAGTCCGTGGATGGGAG

Basic information

species Oryza sativa
transcript LOC_Os02g41590.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g41590.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G540538_T01 (Zea mays), 3'ss of exon 9
atagttctgtcatgtcattgagggctttctgttatctctgttcattcattatattgatttatggtcatgtt---gaaggtaagctc---acttgctactaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAAAGTCCGTGGATGGGAG
       ||      |        || | || | |  |||| ||| |||| ||| ||||     |||| ||   |||  || | |    ||||  ||| ||| ||||| ||  |||||||||||||| |||||||| || ||||  |||||||| |||||| | |||||||||
-----catgaaggaccccgacctactatgtgct-ttgctgtccatgcattttatggattctaaatcatttttttgaatatatggttgctacttattacaaatatagGTATGCTGACTACATCTTCGGCAACGAAACTGAGGCAAAGATCTTTGCCAAAGTCAGAGGATGGGAG
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|38482919|gb|CF966721.1|CF966721
EST:     GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC                         GTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|33690915|gb|CF319154.1|CF319154
EST:     CCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC                         GTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: CCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|87006970|gb|CI275278.1|CI275278
EST:     CCCAGGAGAAGGTTCTTCC                         GTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: CCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|89167316|gb|CI252847.1|CI252847
EST:     GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC                         GTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|87026580|gb|CI252534.1|CI252534
EST:     GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC                         GTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|88725620|gb|CI748879.1|CI748879
EST:     TGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC                         GTCTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: TGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|58600653|gb|CK011181.1|CK011181
EST:     TCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC                         GTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: TCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|300215864|gb|HO088490.1|HO088490
EST:     GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC                         GTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|88983145|gb|CI020709.1|CI020709
EST:     GAGAAGGTTCTTCC                         GTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: GAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|86511587|gb|CI154220.1|CI154220
EST:     TGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC                         GTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: TGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|33800932|gb|CF326339.1|CF326339
EST:     CTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC                         GTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: CTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|38470488|gb|CF954619.1|CF954619
EST:     GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC                         GTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|89199046|gb|CI253120.1|CI253120
EST:     GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC                         GTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|30227286|gb|CB965178.1|CB965178
EST:     GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC                         GTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|66922324|gb|CX109172.1|CX109172
EST:     GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC                         GTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: GCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|33805852|gb|CF328805.1|CF328805
EST:     CTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC                         GTTTGAGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: CTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|86601408|gb|CI253736.1|CI253736
EST:     TGATGCCCAGGAGAAGGTTCTTCC                         GTTTTTGTACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: TGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
EST: gi|38473896|gb|CF958028.1|CF958028
EST:     GAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCC                         GTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA
genomic: GAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 32 (downstream exon)
Score: 95

GTGTTCCTGATGAACCTCTCTGCACCCTTTATCTGTGAGTTTTTCCGTGATGCCCAGGAGAAGGTTCTTCCgtaagtgata ... actaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAAAGTCCGTGGATGGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcattatattgatttatggtcatgttgaaggtaagctcacttgctactaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAAAGTCCGTGGATGGGAG
                                            tactaat  putative branch site (score: 95)
     atattgatttat  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atagttctgtcatgtcattgagggctttctgttatctctgttcattcattatattgatttatggtcatgttgaaggtaagctcacttgctactaatgtagGTTTGTGGACTACATCTTCGGTAACGAAACAGAAGCAAGAATCTTTGCTAAAGTCCGTGGATGGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - -tgtcatg
- - - - - - - - - - - - ctttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacttgc